#!/usr/bin/env python

"""Demonstrates access to UMLS via CTAKES.

"""

__author__ = 'Paul Landes'

from dataclasses import dataclass, field

from pathlib import Path

import pandas as pd

from zensols.cli import CliHarness, ProgramNameConfigurator

from zensols.mednlp.ctakes import CTakesParserStash

# the definition of the application class executed from the CLI glue code

@dataclass

class Application(object):

    """Demonstrates how to use the cTAKES application wrapper.

    """

    # tell the application not mistake the `uts_client` as an option when

    # generating the online help with the -h option

    CLI_META = {'option_excludes': {'ctakes_stash'}}

    ctakes_stash: CTakesParserStash = field()

    """Runs the cTAKES CUI entity linker on a directory of medical notes."""

    def entities(self, sent: str = None, output: Path = None):

        """Parse a sentence and print cTAKES entities.

        :param sent: the sentence to parse and generate features

        """

        if sent is None:

            sent = 'He was diagnosed with kidney failure in the United States.'

        self.ctakes_stash.set_documents([sent])

        df: pd.DataFrame = self.ctakes_stash['0']

        print(df)

        if output is not None:

            df.to_csv(output)

            print(f'wrote: {output}')

if (__name__ == '__main__'):

    CliHarness(

        app_config_resource='ctakes.conf',

        app_config_context=ProgramNameConfigurator(

            None, default='ctakes').create_section(),

        proto_args='',

        proto_factory_kwargs={'reload_pattern': '^ctakes'},

    ).run()